Cancer diagnosis marker extraction for soft tissue sarcomas based on gene expression profiling data by using projective adaptive resonance theory (PART) filtering method

BACKGROUND: Recent advances in genome technologies have provided an excellent opportunity to determine the complete biological characteristics of neoplastic tissues, resulting in improved diagnosis and selection of treatment. To accomplish this objective, it is important to establish a sophisticated algorithm that can deal with large quantities of data such as gene expression profiles obtained by DNA microarray analysis. RESULTS: Previously, we developed the projective adaptive resonance theory (PART) filtering method as a gene filtering method. This is one of the clustering methods that can select specific genes for each subtype. In this study, we applied the PART filtering method to analyze microarray data that were obtained from soft tissue sarcoma (STS) patients for the extraction of subtype-specific genes. The performance of the filtering method was evaluated by comparison with other widely used methods, such as signal-to-noise, significance analysis of microarrays, and nearest shrunken centroids. In addition, various combinations of filtering and modeling methods were used to extract essential subtype-specific genes. The combination of the PART filtering method and boosting – the PART-BFCS method – showed the highest accuracy. Seven genes among the 15 genes that are frequently selected by this method – MIF, CYFIP2, HSPCB, TIMP3, LDHA, ABR, and RGS3 – are known prognostic marker genes for other tumors. These genes are candidate marker genes for the diagnosis of STS. Correlation analysis was performed to extract marker genes that were not selected by PART-BFCS. Sixteen genes among those extracted are also known prognostic marker genes for other tumors, and they could be candidate marker genes for the diagnosis of STS. CONCLUSION: The procedure that consisted of two steps, such as the PART-BFCS and the correlation analysis, was proposed. The results suggest that novel diagnostic and therapeutic targets for STS can be extracted by a procedure that includes the PART filtering method

Renewal Equations Applied to Evaluation of Interventions for the Control and Prevention of Infectious Diseases

Control and prevention of infectious disease prevalence have been a priority to reduce the burden (mortality and morbidity) of the diseases. Mathematical modeling has been used to study the direct and indirect effect of Infection Prevention and Control (IPC) measures on the disease transmission dynamics and to estimate the cost effectiveness of immunization programs including vaccine production and immunization program design and implementation. However, for more efficient programs regarding IPC priority policies and in order to optimize the limited available resources for the control of infectious diseases, more rigorous mathematical models and analyses are required. This dissertation is dedicated to the development of a mathematical framework using delay systems (delay/functional differential equations and Volterra integral equations of second type) to examine the effectiveness of control and prevention interventions for infectious diseases. The framework enables us to formulate and derive mathematical and epidemiological analyses of a wide range of compartmental models that have been traditionally studied using ordinary, partial and delay differential equations. We specifically use this framework to address heterogeneity in the population and to better understand the disease dynamics and the burden of the disease with and without interventions. We also use this framework to study vertical transmission and vector-borne diseases

Combating cyber attacks in cloud computing using machine learning techniques.

An extensive investigative survey on Cloud Computing with the main focus on gaps that is slowing down Cloud adoption as well as reviewing the threat remediation challenges. Some experimentally supported thoughts on novel approaches to address some of the widely discussed cyber-attack types using machine learning techniques. The thoughts have been constructed in such a way so that Cloud customers can detect the cyber-attacks in their VM without much help from Cloud service provide

Parameter-free agglomerative hierarchical clustering to model learners' activity in online discussion forums

L'anàlisi de l'activitat dels estudiants en els fòrums de discussió online implica un problema de modelització altament depenent del context, el qual pot ser plantejat des d'aproximacions tant teòriques com empíriques. Quan aquest problema és abordat des de l'àmbit de la mineria de dades, l'enfocament més comunament adoptat és el de la classificació no supervisada (o clustering), donant lloc, d'aquesta manera, a un escenari de clustering en el qual el nombre real de clústers és a priori desconegut. Per tant, aquesta aproximació revela una qüestió subjacent, la qual no és sinó un dels problemes més coneguts del paradigma del clustering: l'estimació del nombre de clústers, habitualment seleccionat per l'usuari concorde a algun tipus de criteri subjectiu que pot comportar fàcilment l'aparició de biaixos indesitjats en els models obtinguts. Amb l'objectiu d'evitar qualsevol intervenció de l'usuari en l'etapa de clustering, dos nous criteris d'unió entre clústers són proposats en la present tesi, els quals, al seu torn, permeten la implementació d'un nou algorisme de clustering jeràrquic aglomeratiu lliure de paràmetres. Un complet conjunt d'experiments indica que el nou algorisme de clustering és capaç de proporcionar solucions de clustering òptimes enfront d'una gran varietat d'escenaris de clustering, sent capaç de bregar amb diferents classes de dades, així com de millorar el rendiment ofert pels algorismes de clustering més àmpliament emprats en la pràctica. Finalment, una estratègia d'anàlisi de dues etapes basada en el paradigma del clustering subespaial és proposada a fi d'abordar adequadament el problema de la modelització de la participació dels estudiants en les discussions asíncrones. Combinada amb el nou algorisme clustering, l'estratègia proposada demostra ser capaç de limitar la intervenció subjectiva de l'usuari a les etapes d'interpretació del procés d'anàlisi i de donar lloc a una completa modelització de l'activitat duta a terme pels estudiants en els fòrums de discussió online.El análisis de la actividad de los estudiantes en los foros de discusión online acarrea un problema de modelización altamente dependiente del contexto, el cual puede ser planteado desde aproximaciones tanto teóricas como empíricas. Cuando este problema es abordado desde el ámbito de la minería de datos, el enfoque más comúnmente adoptado es el de la clasificación no supervisada (o clustering), dando lugar, de este modo, a un escenario de clustering en el que el número real de clusters es a priori desconocido. Por tanto, esta aproximación revela una cuestión subyacente, la cual no es sino uno de los problemas más conocidos del paradigma del clustering: la estimación del número de clusters, habitualmente seleccionado por el usuario acorde a algún tipo de criterio subjetivo que puede conllevar fácilmente la aparición de sesgos indeseados en los modelos obtenidos. Con el objetivo de evitar cualquier intervención del usuario en la etapa de clustering, dos nuevos criterios de unión entre clusters son propuestos en la presente tesis, los cuales, a su vez, permiten la implementación de un nuevo algoritmo de clustering jerárquico aglomerativo libre de parámetros. Un completo conjunto de experimentos indica que el nuevo algoritmo de clustering es capaz de proporcionar soluciones de clustering óptimas frente a una gran variedad de escenarios de clustering, siendo capaz de lidiar con diferentes clases de datos, así como de mejorar el rendimiento ofrecido por los algoritmos de clustering más ampliamente utilizados en la práctica. Finalmente, una estrategia de análisis de dos etapas basada en el paradigma del clustering subespacial es propuesta a fin de abordar adecuadamente el problema de la modelización de la participación de los estudiantes en las discusiones asíncronas. Combinada con el nuevo algoritmo clustering, la estrategia propuesta demuestra ser capaz de limitar la intervención subjetiva del usuario a las etapas de interpretación del proceso de análisis y de dar lugar a una completa modelización de la actividad llevada a cabo por los estudiantes en los foros de discusión online.The analysis of learners' activity in online discussion forums leads to a highly context-dependent modelling problem, which can be posed from both theoretical and empirical approaches. When this problem is tackled from the data mining field, a clustering-based perspective is usually adopted, thus giving rise to a clustering scenario where the real number of clusters is a priori unknown. Hence, this approach reveals an underlying problem, which is one of the best-known issues of the clustering paradigm: the estimation of the number of clusters, habitually selected by user according to some kind of subjective criterion that may easily lead to the appearance of undesired biases in the obtained models. With the aim of avoiding any user intervention in the cluster analysis stage, two new cluster merging criteria are proposed in the present thesis, which allow to implement a novel parameter-free agglomerative hierarchical algorithm. A complete set of experiments indicate that the new clustering algorithm is able to provide optimal clustering solutions in the face of a great variety of clustering scenarios, both having the ability to deal with different kinds of data and outperforming clustering algorithms most widely used in practice. Finally, a two-stage analysis strategy based on the subspace clustering paradigm is proposed to properly tackle the issue of modelling learners' participation in the asynchronous discussions. In combination with the new clustering algorithm, the proposed strategy proves to be able to limit user's subjective intervention to the interpretation stages of the analysis process and to lead to a complete modelling of the activity performed by learners in online discussion forums